2db3

About this Structure
2DB3 is a 8 chains structure of sequences from Drosophila melanogaster. Full crystallographic information is available from OCA.

The crystallographic asymmetric unit of the solved structure contains 4 monomers of Vasa.

Each monomer of Vasa in the structure is bound to RNA and an ATP analog; this is presumed to represent the biological molecule.

Each monomer of Vasa has an N-terminal domain that binds the 3' side of the RNA and a C-terminal domain that binds the 5' side of the RNA.

The 11 conserved motifs colored according to figure 1 of the paper describing the structure. .

The wedge helix (overlapping with Motif Ib) clashes with the RNA continuing on in normal helix and forces a bend between nucleotide 5 and 6 in the structure. [ Note: this view generates a surface area which may take half a minute to calculate. ]

Motifs I and II bind the triphosphate of the ATP analog directly and through a magnesium ion and water. A red broken line connects the gamma-phosphorous atom and a well-ordered water located ~3.25&Aring; away, situated ideally for a nucleophilic in-line attack. Two arginines and a histidine shield the active site from the negative charge of the phosphates. Gln272 recognizes the adenosine base moiety, specifying ATP vs. GTP.

Reference
Original page seeded by OCA on Tue Feb 17 20:22:33 2009